DNA and Double Up (R. Kelly album): Difference between pages

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{{future album}}

:''For other uses, see [[DNA (disambiguation)]].''

{{Infobox Album <!-- See Wikipedia:WikiProject_Albums -->

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| Name = Double Up

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| Type = [[Album]]

[[Image:DNA_Overview.png|thumb|270px|The general structure of a section of DNA]]

| Artist = [[R. Kelly]]

'''Deoxyribonucleic acid''' ('''DNA''') is a [[nucleic acid]] &mdash;usually in the form of a double [[helix]]&mdash; that contains the [[genetics|genetic]] instructions specifying the [[developmental biology|biological development]] of all [[Cell (biology)|cellular]] forms of [[life]], and most [[virus]]es. DNA is a long [[polymer]] of [[nucleotides]] (a polynucleotide) and encodes the sequence of the [[amino acid residue]]s in [[protein]]s using the [[genetic code]], a [[triplet code]] of [[nucleotide]]s.

| Cover = DoubleUp.JPG

| Released = [[May 29]], [[2007]]

In complex [[eukaryote|eukaryotic]] [[Cell (biology)|cells]] such as those from [[plant]]s, [[animal]]s, [[fungi]] and [[protist]]s, most of the DNA is located in the [[cell nucleus]]. By contrast, in simpler cells called [[prokaryotes]], including the [[bacterium|eubacteria]] and [[archaea]], DNA is not separated from the [[cytoplasm]] by a [[nuclear envelope]]. The cellular [[organelle]]s known as [[chloroplast]]s and [[mitochondria]] also carry DNA.

| Recorded =

| Genre = [[Urban contemporary|Urban]]<br>[[hip hop music|Hip hop]]<br>[[Pop-Rap]]

DNA is often referred to as the molecule of [[heredity]] as it is responsible for the genetic propagation of most [[biological inheritance|inherited]] [[Trait (biological)|trait]]s. In humans, these traits can range from hair colour to disease susceptibility. During [[cell division]], DNA is [[DNA replication|replicated]] and can be transmitted to offspring during [[reproduction]]. [[Kinship and descent|Lineage]] studies can be done based on the facts that the [[mitochondrial DNA]] only comes from the mother, and the male [[Y chromosome]] only comes from the father.

| Length =

| Label = [[Jive Records]]

Every person's DNA, their [[genome]], is inherited from both parents. The mother's [[mitochondrial DNA]] together with twenty-three [[chromosome]]s from each parent combine to form the genome of a [[zygote]], the [[fertilization|fertilized]] [[ovum|egg]]. As a result, with certain exceptions such as [[red blood cell]]s, most human cells contain 23 pairs of chromosomes, together with mitochondrial DNA inherited from the mother.

| Producer = [[R. Kelly]]<br>[[The Neptunes]]<br>[[Dr.Dre]]<br>[[Kanye West]]<br>[[The Runners]]<br>[[Just Blaze]]

| Reviews =

==Overview==

| Last album = ''[[Remix City Vol. 1]]''<br />(2005)

[[Image:DNA-fragment-3D-vdW.png|thumb|right|150px|Space-filling model of a section of DNA molecule]]

| This album = '''''Double Up'''''<br />(2007)

[[Image:Dna_pairing_aa.gif|thumb|300px|DNA base pairing]]

Contrary to a common misconception, the DNA is not a single [[molecule]], but rather a pair of molecules joined by [[hydrogen bond]]s: it is organized as two complementary strands, head-to-toe, with the hydrogen bonds between them.<ref name=Butler>Butler, John M. (2001) ''Forensic DNA Typing'' "Elsevier". pp. 14-15. ISBN 012147951X.</ref> Each strand of DNA is a chain of chemical "building blocks", called [[nucleotide]]s, of which there are four types: [[adenine]] (abbreviated A), [[cytosine]] (C), [[guanine]] (G) and [[thymine]] (T).<ref name=Butler /> (Thymine should not be confused with [[thiamine]], which is vitamin B₁.) In some organisms, most notably the PBS1 [[phage]], [[Uracil]] (U) replaces T in the organism's DNA.<ref>I. Takahashi and J. Marmur. Replacement of thymidylic acid by deoxyuridylic acid in the deoxyribonucleic acid of a transducing phage for Bacillus subtilis. ''Nature'' 197, 794&ndash;795, 1963.</ref> These allowable base components of nucleic acids can be [[polymerized]] in any order giving the molecules a high degree of uniqueness.

Between the two strands, each base can only "pair up" with one single predetermined other base: A+T, T+A, C+G and G+C are the only possible combinations; that is, an "A" on one strand of double-stranded DNA will "mate" properly only with a "T" on the other, complementary strand; therefore, naming the bases on the conventionally chosen side of the strand is enough to describe the entire double-strand sequence.<ref name=Butler /> Two nucleotides paired together are called a [[base pair]]. On rare occasions, wrong pairing can happen, when [[thymine]] goes into its [[enol]] form or [[cytosine]] goes into its [[imino]] form. The double-stranded structure of DNA provides a simple mechanism for [[DNA replication]]: the DNA double strand is first "unzipped" down the middle, and the "other half" of each new single strand is recreated by exposing each half to a mixture of the four bases. An enzyme makes a new strand by finding the correct base in the mixture and pairing it with the original strand. In this way, the base on the old strand dictates which base will be on the new strand, and the cell ends up with an extra copy of its DNA.

DNA contains the genetic [[information]] that is inherited by the offspring of an organism; this information is determined by the [[DNA sequence|sequence]] of base pairs along its length. A strand of DNA contains [[gene]]s, areas that [[gene regulation|regulate genes]], and areas that either have no function, or a function [[junk DNA|yet unknown]]. Genes can be loosely viewed as the organism's "cookbook" or "blueprint".

[[Image:DNA Under electron microscope Image 3576B-PH.jpg|thumb|left|250px|DNA Under an electron microscope]]

Other interesting points:

* DNA is an acid because of the phosphate groups between each deoxyribose. This is the primary reason why DNA has a negative charge.

* The "polarity" of each pair is important: A+T is not the same as T+A, just as C+G is not the same as G+C (note that "polarity" as such is never used in this context -- it's just a suggestive way to get the idea across).

* [[Mutation]]s are the results of the cells' attempts to repair chemical imperfections in this process, where a base is accidentally skipped, inserted, or incorrectly copied, or the chain is trimmed, or added to. Many mutations can be described as combinations of these accidental "operations". Mutations can also occur after chemical damage (through [[mutagens]]), light ([[Ultraviolet|UV]] damage), or through other more complicated gene swapping events.

*[[Deoxyribozyme|DNA molecules that act as enzymes]] are known in laboratories, but none have been known to be found in life so far.

* In addition to the traditionally viewed duplex form of DNA, DNA can also acquire triplex and quadruplex forms. Here instead of the Watson-Crick base pairing, [[Hoogsteen base pair|Hoogsteen base pairing]] comes into the picture.

* DNA differs from [[ribonucleic acid]] (RNA) by having a sugar 2-deoxyribose instead of [[ribose]] in its backbone. This is the basic chemical distinction between RNA and DNA. In addition, in most{{citeneeded}} RNA, the nucleotides [[thymine]] (T) are replaced by [[uracil]] (U).

==DNA in practice==

===DNA in crime===

{{main|Genetic fingerprinting}}

[[Forensic science|Forensic scientists]] can use DNA located in [[blood]], [[semen]], [[skin]], [[saliva]] or hair left at the scene of a crime to identify a possible suspect, a process called [[genetic fingerprinting]] or DNA profiling. In DNA profiling the relative lengths of sections of repetitive DNA, such as [[short tandem repeats]] and [[minisatellite]]s, are compared. DNA profiling was developed in 1984 by English geneticist [[Alec Jeffreys]] of the [[University of Leicester]], and was first used to convict Colin Pitchfork in 1988 in the [[Enderby murders]] case in [[Leicestershire]], [[England]]. Many jurisdictions require convicts of certain types of crimes to provide a sample of DNA for inclusion in a computerized database. This has helped investigators solve old cases where the perpetrator was unknown and only a DNA sample was obtained from the scene (particularly in [[rape]] cases between strangers). This method is one of the most reliable techniques for identifying a criminal, but is not always perfect, for example if no DNA can be

retrieved, or if the scene is contaminated with the DNA of several possible suspects. It is also called the strand of life.

===DNA in computation ===

DNA plays an important role in [[computer science]], [[Bioinformatics| bioinformatics and computational biology]], both as a motivating research problem and as a method of computation in itself.

Research on [[string searching algorithm]]s, which find an occurrence of a sequence of letters inside a larger sequence of letters, was motivated in part by DNA research, where it is used to find specific sequences of nucleotides in a large sequence.<ref>Gusfield, Dan. ''Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology''. Cambridge University Press, 15 January [[1997]]. ISBN 0521585198.</ref> In other applications such as [[text editor]]s, even simple algorithms for this problem usually suffice, but DNA sequences cause these algorithms to exhibit near-worst-case behavior due to their small number of distinct characters.

[[Database]] theory has been influenced by DNA research, which poses special problems for storing and manipulating DNA sequences. Databases specialized for DNA research are called [[genomic database]]s, and must address a number of unique technical challenges associated with the operations of approximate matching, sequence comparison, finding repeating patterns, and homology searching.

In 1994, [[Leonard Adleman]] of the [[University of Southern California]] made headlines when he discovered a way of solving the directed [[Hamiltonian path problem]], an [[NP-complete]] problem, using tools from molecular biology, in particular DNA. The new approach, dubbed [[DNA computing]], has practical advantages over traditional computers in power use, space use, and efficiency, due to its ability to highly parallelize the computation (see [[parallel computing]]), although there is labor worth mentioning involved in retrieving the answers. A number of other problems, including simulation of various [[abstract machine]]s, the [[boolean satisfiability problem]], and the bounded version of the [[Post correspondence problem]], have since been analyzed using DNA computing.

Due to its compactness, DNA also has a theoretical role in [[cryptography]], where in particular it allows unbreakable [[one-time pad]]s to be efficiently constructed and used.<ref>Ashish Gehani, Thomas LaBean and John Reif. [http://citeseer.ist.psu.edu/gehani99dnabased.html DNA-Based Cryptography].

Proceedings of the 5th DIMACS Workshop on DNA Based Computers, Cambridge, MA, USA, 14&ndash;15 June 1999.</ref>

=== DNA in historical and anthropological study ===

Because DNA collects mutations over time, which are then passed down from parent to offspring, it contains information about processes that have occurred in the past. By comparing different DNA sequences, geneticists can attempt to infer the history of organisms.

If DNA sequences from different [[species]] are compared, then the resulting family tree, or [[phylogeny]] can be used to study the [[evolution]] of these species. This field of [[phylogenetics]] is a powerful tool in [[evolutionary biology]]. If DNA sequences within a species are compared, [[population genetics|population geneticists]] can glean information on the history of particular populations. This can be used in studies ranging from [[ecological genetics]] to [[anthropology]] (for example, DNA evidence is also being used to try to identify the [[Ten Lost Tribes of Israel]]<ref>''Lost Tribes of Israel'', [[NOVA (TV series)|NOVA]], PBS airdate: 22 February 2000. Transcript available from http://www.pbs.org/wgbh/nova/transcripts/2706israel.html (last accessed on 4 March 2006)</ref><ref>{{cite web| url=http://www.aish.com/societywork/sciencenature/the_cohanim_-_dna_connection.asp| title=The Cohanim/DNA Connection| first= Yaakov | last=Kleiman| accessdate=2006-03-04}}</ref>).

DNA has also been used to look at fairly recent issues of family relationships, such as establishing some manner of familial relationship between the descendants of [[Sally Hemings]] and the family of [[Thomas Jefferson]]. This usage is closely related to the use of DNA in criminal investigations detailed above. Indeed, some criminal investigations have been solved when DNA from crime scenes has fortuitously matched relatives of the guilty individual.[http://www.newscientist.com/article.ns?id=dn4908][http://news.bbc.co.uk/1/hi/wales/3044282.stm]

==Molecular structure==

[[Image:NA-comparedto-DNA thymineAndUracilCorrected.png|right|400px|thumb|Comparisons between DNA and single stranded RNA with the diagram of the bases showing.]]

Although sometimes called "the molecule of heredity", DNA macromolecules as people typically think of them are not single molecules. Rather, they are pairs of molecules, which entwine like vines to form a '''double [[helix]]''' (see the illustration at the right).

Each vine-like molecule is a strand of DNA: '''a chemically linked chain of [[nucleotide]]s, each of which consists of a [[sugar]] ([[deoxyribose]]), a [[phosphate]] and one of five kinds of [[nucleobase]]s ("bases")'''. Because DNA strands are composed of these nucleotide subunits, they are [[polymer]]s.

The diversity of the bases means that there are five kinds of nucleotides, which are commonly referred to by the identity of their bases. These are [[adenine]] (A), [[thymine]] (T), [[uracil]] (U), [[cytosine]] (C), and [[guanine]] (G). U is rarely found in DNA except as a result of chemical degradation of C, but in some viruses, notably PBS1 phage DNA, U completely replaces the usual T in its DNA. Similarly, RNA usually contains U in place of T, but in certain RNAs such as [[transfer RNA]], T is always found in some positions. Thus, the only true difference between DNA and RNA is the sugar, 2-deoxyribose in DNA and ribose in RNA.

In a DNA double helix, two polynucleotide strands can associate through the [[hydrophobic effect]] and [[pi stacking]]. Specificity of which strands stay associated is determined by [[base pair|complementary pairing]]. Each base forms [[hydrogen bond]]s readily to only one other, A to T forming two hydrogen bonds and C to G forming three hydrogen bonds. The GC content and length of each DNA molcule dictates the strength of the association; the more complementary bases exist, the stronger and longer-lasting the association characterised by the temperate required to break the hydrogen bonding, its [[Melting temperature|T_m]] value.

The cell's machinery is capable of ''melting'' or disassociating a DNA double helix, and using each DNA strand as a template for synthesizing a new strand which is nearly identical to the previous strand. Errors that occur in the synthesis are known as [[mutations]]. The process known as [[Polymerase chain reaction|PCR]] (polymerase chain reaction) mimics this process [[in vitro]] in a nonliving system.

Because pairing causes the nucleotide bases to face the helical axis, the sugar and phosphate groups of the nucleotides run along the outside; the two chains they form are sometimes called the "'''backbones'''" of the helix. In fact, it is chemical bonds between the phosphates and the sugars that link one nucleotide to the next in the DNA strand.

{{multi-video start}}

{{multi-video item |

filename = ADN animation.gif |

title = Rotating DNA stick model |

description = Animation of a section of DNA rotating. (1.00 [[Megabyte|MB]], [[animated GIF]] format). |

format = [[animated GIF]]

}}

{{multi-video end}}

'''''Double Up''''' is [[R. Kelly]]'s latest album. The album's first single, "[[I'm a Flirt|I'm a Flirt (Remix)]]" featuring [[T.I.]], and [[T-Pain]] has been gaining momentum on the Billboard Top 40 charts and continues to top radio and video countdown shows including BET's [[106 & Park]].

==Sequence role==

Within a gene, the sequence of [[nucleotides]] along a DNA strand defines a messenger RNA sequence which then defines a [[protein]], that an [[organism]] is liable to manufacture or "[[gene expression|express]]" at one or several points in its life using the information of the sequence. The relationship between the nucleotide sequence and the [[amino acid|amino-acid]] sequence of the protein is determined by simple cellular rules of [[Translation (genetics)|translation]], known collectively as the [[genetic code]]. The genetic code consists of three-letter 'words' (termed a codon) formed from a sequence of three nucleotides (e.g. ACT, CAG, TTT). These codons can then be translated with [[messenger RNA]] and then [[transfer RNA]], with a codon corresponding to a particular amino acid. There are 64 possible codons (4 bases in 3 places <math>4^3</math>) that encode 20 amino acids. Most amino acids, therefore, have more than one possible codon. There are also three 'stop' or 'nonsense' codons signifying the end of the coding region, namely the UAA, UGA and UAG codons.

Kelly revealed that the album is set to feature guest appearances & production by [[The Neptunes]], [[The Runners]], Mysto & Pizzi, [[Kanye West]], [[Young Jeezy]], [[Snoop Dogg]], [[Rick Ross]], [[T.I.]] & [[T-Pain]]. He explains that due to the success of his current collaborations with rappers like Young Jeezy and Ludacris, he thought, "why not put some of that magic on my album?" Well, Kelly didn't just put some of what he calls "magic" on the album, during the phone recording, he says 70 percent of the record will be up tempo but he assures fans that "there will be some slow jams on there."

In many [[species]], only a small fraction of the total sequence of the [[genome]] appears to encode protein. For example, only about 1.5% of the [[human genome]] consists of protein-coding [[exons]]. The function of the rest is a matter of speculation. It is known that certain nucleotide sequences specify affinity for [[DNA binding protein]]s, which play a wide variety of vital roles, in particular through control of replication and transcription. These sequences are frequently called [[regulatory sequence]]s, and researchers assume that so far they have identified only a tiny fraction of the total that exist. "[[Junk DNA]]" represents sequences that do not yet appear to contain genes or to have a function. The reasons for the presence of so much [[non-coding DNA]] in [[eukaryotic]] genomes and the extraordinary differences in [[genome size]] ("[[C-value]]") among species represent a long-standing puzzle in DNA research known as the "[[C-value enigma]]".

Some DNA sequences play structural roles in chromosomes. [[Telomere]]s and [[centromere]]s typically contain few (if any) protein-coding genes, but are important for the function and stability of chromosomes. Some genes code for "RNA genes" (see [[tRNA]] and [[rRNA]]). Some RNA genes code for transcripts that function as regulatory RNAs (see [[RNA interference|siRNA]]) that influence the function of other RNA molecules. The intron-exon structure of some genes (such as immunoglobin and protocadeherin genes) is important for allowing alternative splicing of pre-mRNA which allows several different proteins to be made from the same gene. Some non-coding DNA represents [[pseudogene]]s that can be used as raw material for the creation of new genes with new functions. Some non-coding DNA provided hot-spots for duplication of short DNA regions; such sequence duplication has been the major form of genetic change in the human lineage (see evidence from the [[Chimpanzee Genome Project]]). Exons interspersed with introns allows for "exon shuffling" and the creation of modified genes that might have new adaptive functions. Large amounts of non-coding DNA is probably adaptive in that it provides chromosomal regions where [[Genetic recombination|recombination]] between homologous portions of chromosomes can take place without disrupting the function of genes. Some biologists such as [[Stuart Kauffman]] have speculated that non-coding DNA may modify the rate of evolution of a species.{{citation needed}}

==Track Listing==

Sequence also determines a DNA segment's susceptibility to cleavage by [[restriction enzyme]]s, the quintessential tools of [[genetic engineering]]. The position of cleavage sites throughout an individual's genome determines one kind of an individual's "[[DNA fingerprinting|DNA fingerprint]]".

* "[[I'm a Flirt]] [Remix]" <small>(featuring [[T.I.]] & [[T-Pain]])</small>

==ReplicationTrivia==

* R. Kelly says that this will be his best album out of all nine.

''Main article:'' [[DNA replication]]

[[image:dna-split.png|frame|DNA replication]]

<!-- summary has been added, below, also include any extra context relevant for this article as well

..[[origin of replication]]...chromosome...plasmid...DNA polymerase...[[mutation]]...[a paragraph including these ideas would be useful and go well here]

-->

DNA replication or DNA synthesis is the process of copying the double-stranded DNA prior to [[cell division]]. The two resulting double strands are generally almost perfectly identical, but occasionally errors in replication or exposure to chemicals, or radiation can result in a less than perfect copy (see [[mutation]]), and each of them consists of one original and one newly synthesized strand. This is called ''[[semiconservative replication]]''. The process of replication consists of three steps: ''initiation'', ''elongation'' and ''termination''.

==Mechanical biological properties==

{{main|Mechanical properties of DNA}}

===Strands association and dissociation===

The hydrogen bonds between the strands of the double helix are weak enough that they can be easily separated by [[enzyme]]s. Enzymes known as [[helicase]]s unwind the strands to facilitate the advance of sequence-reading enzymes such as [[DNA polymerase]]. The unwinding requires that helicases chemically cleave the phosphate backbone of one of the strands so that it can swivel around the other. The strands can also be separated by gentle heating, as used in [[PCR]], provided they have fewer than about 10,000 '''base pairs''' (10 kilobase pairs, or 10 kbp). The intertwining of the DNA strands makes long segments difficult to separate.

===Circular DNA===

When the ends of a piece of double-helical DNA are joined so that it forms a circle, as in [[plasmid]] DNA, the strands are [[knot theory|topologically]] knotted. This means they cannot be separated by gentle heating or by any process that does not involve breaking a strand. The task of unknotting topologically linked strands of DNA falls to enzymes known as [[topoisomerase]]s. Some of these enzymes unknot circular DNA by cleaving two strands so that another double-stranded segment can pass through. Unknotting is required for the replication of circular DNA as well as for various types of [[recombination]] in linear DNA.

===Great length versus tiny breadth===

The narrow breadth of the double helix makes it impossible to detect by conventional [[transmission electron microscope|electron microscopy]], except by heavy staining. At the same time, the DNA found in many cells can be macroscopic in length -- approximately 2 [[meter]]s long for strands in a human chromosome.<ref>{{cite web| url=http://hypertextbook.com/facts/1998/StevenChen.shtml| title=Length of a Human DNA Molecule| accessdate=2006-03-04}}</ref> Consequently, cells must compact or "package" DNA to carry it within them. This is one of the functions of the chromosomes, which contain spool-like [[protein]]s known as [[histone]]s, around which DNA winds.

===Entropic stretching behavior===

When DNA is in solution, it undergoes conformational fluctuations due to the energy available in the [[thermal bath]]. For [[Entropy|entropic]] reasons, floppy states are more thermally accessible than stretched out states; for this reason, a single molecule of DNA stretches similarly to a rubber band. Using [[optical tweezers]], the entropic stretching behavior of DNA has been studied and analyzed from a [[polymer physics]] perspective, and it has been found that DNA behaves like the ''Kratky-Porod'' [[worm-like chain]] model with a persistence length of about 53 nm.

Furthermore, DNA undergoes a stretching [[phase transition]] at a force of 65 [[Newtons|pN]]; above this force, DNA is thought to take the form that [[Linus Pauling]] originally hypothesized, with the phosphates in the middle and bases splayed outward. This proposed structure for overstretched DNA has been called "P-form DNA," in honor of Pauling.

===Different helix geometries===

The DNA helix can assume one of three slightly different geometries, of which the "B" form described by [[James D. Watson]] and [[Francis Crick]] is believed to predominate in cells. It is 2 [[nanometre]]s wide and extends 3.4 nanometres per 10 [[Base pair|bp]] of sequence. This is also the approximate length of sequence in which the double helix makes one complete turn about its axis. This frequency of twist (known as the helical ''pitch'') depends largely on stacking forces that each base exerts on its neighbors in the chain.

====Supercoiled DNA====

{{main|Supercoil}}

The B form of the DNA helix twists 360° per 10 bp in the absence of strain. But many molecular biological processes can induce strain. A DNA segment with excess or insufficient helical twisting is referred to, respectively, as positively or negatively "supercoiled". DNA ''in vivo'' is typically negatively supercoiled, which facilitates the unwinding of the double-helix required for [[transcription (genetics)|RNA transcription]].

====Sugar pucker====

There are four conformations that the [[ribofuranose]] rings in nucleotides can acquire:

# C-2' endo

# C-2' exo

# C-3' endo

# C-3' exo

Ribose is usually in C-3'endo, while deoxyribose is usually in the C-2' endo sugar pucker conformation.

The A and B forms differ mainly in their ''sugar pucker''. In the A form, the C3' configuration is above the sugar ring, whilst the C2' configuration is below it. Thus, the A form is described as "C3'-endo." Likewise, in the B form, the C2' configuration is above the sugar ring, whilst C3' is below; this is called "C2'-endo." Altered sugar puckering in A-DNA results in shortening the distance between adjacent phosphates by around one angstrom. This gives 11 to 12 base pairs to each helix in the DNA strand, instead of 10.5 in B-DNA. Sugar pucker gives uniform ribbon shape to DNA, a cylindrical open core, and also a deep major groove more narrow and pronounced that grooves found in B-DNA.

====A and Z helices formation====

The two other known double-helical forms of DNA, called A and [[Z-DNA|Z]], differ modestly in their geometry and dimensions. The A form appears likely to occur only in dehydrated samples of DNA, such as those used in [[crystallography|crystallographic]] experiments, and possibly in hybrid pairings of DNA and [[RNA]] strands. Segments of DNA that cells have [[methylation|methylated]] for regulatory purposes may adopt the Z geometry, in which the strands turn about the helical axis like a mirror image of the B form.

====Properties of different helical forms====

{| border="0" align="center" style="border: 1px solid #999; background-color:#FFFFFF"

|-align="center" bgcolor="#CCCCCC"

!Geometry attribute

!A-form

!B-form

!Z-form

|-

|Helix sense ||align="center"| right-handed ||align="center"| right-handed ||align="center"| left-handed

|--bgcolor="#EFEFEF"

|Repeating unit ||align="right"| 1 bp ||align="right"| 1 bp ||align="right"| 2 bp

|-----

|Rotation/bp ||align="right"| 33.6° ||align="right"| 35.9° ||align="right"| 60°/2

|--bgcolor="#EFEFEF"

|Mean bp/turn ||align="right"| 10.7 ||align="right"| 10.4 ||align="right"| 12

|-----

|Inclination of bp to axis ||align="right"| +19° ||align="right"| -1.2° ||align="right"| -9°

|--bgcolor="#EFEFEF"

|Rise/bp along axis ||align="right"| 0.23 nm ||align="right"| 0.332 nm ||align="right"| 0.38 nm

|-----

|Pitch/turn of helix ||align="right"| 2.46 nm ||align="right"| 3.32 nm ||align="right"| 4.56 nm

|--bgcolor="#EFEFEF"

|Mean propeller twist ||align="right"| +18° ||align="right"| +16° ||align="right"| 0°

|-----

|Glycosyl angle ||align="center"| anti ||align="center"| anti ||align="center"| C: anti,<br> G: syn

|--bgcolor="#EFEFEF"

|Sugar pucker ||align="center"| C3'-endo ||align="center"| C2'-endo ||align="center"| C: C2'-endo,<br>G: C2'-exo

|-----

|Diameter ||align="right"| 2.55 nm ||align="right"| 2.37 nm ||align="right"| 1.84 nm

|--bgcolor="#EFEFEF"

|}

===Non-helical forms===

There is an argument to be made that the native, intracellular form of DNA is not the B-form double helix, as commonly supposed. Rather, this argument proposes, the strands of DNA remain almost entirely separate in their normal states.

Information on this alternative theory is available from this online book, presented in PDF format:

http://www.notahelix.com/delmonte/new_struct_mol_biol.pdf

and a recent research paper summarises some key experimental data which are better explained by SBS models than by the double helix:

http://www.ias.ac.in/currsci/dec102003/1564.pdf

with subsequent correspondence:

http://www.ias.ac.in/currsci/may252004/1352.pdf

However, these theories have problems of their own, such as explaining the near-perfect symmetry of DNA in cells and the activity of DNA repair in the absence of a base-paired strand for comparison. Additionally, the activity of [[topoisomerase|topoisomerases]] would be entirely redundant, and not nearly as important to cellular function as it patently is, if not for the fact that base-paired double-strands are at least the primary form of cellular DNA.

==Strand direction==

The asymmetric shape and linkage of nucleotides means that a DNA strand always has a discernible orientation or directionality. Because of this directionality, close inspection of a double helix reveals that nucleotides are heading one way along one strand (the "''ascending strand''"), and the other way along the other strand (the "''descending strand''"). This arrangement of the strands is called '''antiparallel'''.

===Chemical nomenclature ([[5' end|5']] and [[3' end|3']])===

For reasons of chemical nomenclature, people who work with DNA refer to the asymmetric ends of ("five prime" and "three prime"). Within a cell, the enzymes that perform [[DNA replication|replication]] and [[DNA transcription|transcription]] read DNA in the "'''[[3' end|3']] to [[5' end|5']] direction'''", while the enzymes that perform translation read in the opposite directions (on [[RNA|RNA]]). However, because chemically produced DNA is synthesized and manipulated in the opposite or in non-directional manners, the orientation should not be assumed. In a vertically oriented double helix, the [[3' end|3']] strand is said to be ascending while the [[5' end|5']] strand is said to be descending.

===Sense and antisense===

As a result of their antiparallel arrangement and the sequence-reading preferences of enzymes, even if both strands carried identical instead of complementary sequences, cells could properly translate only one of them. The other strand a cell can only read backwards. [[molecular biology|Molecular biologists]] call a sequence "'''sense'''" if it is translated or translatable, and they call its complement "'''antisense'''". It follows then, somewhat paradoxically, that the template for transcription is the ''antisense'' strand. The resulting transcript is an RNA replica of the ''sense'' strand and is itself ''sense.''

===Distinction between sense and antisense strands===

A small proportion of genes in [[prokaryotes]], and more in [[plasmids]] and [[viruses]], blur the distinction made above between sense and antisense strands. Certain sequences of their [[genome|genomes]] do double duty, encoding one protein when read 5' to 3' along one strand, and a second protein when read in the opposite direction (still 5' to 3') along the other strand. As a result, the genomes of these viruses are unusually compact for the number of genes they contain, which biologists view as an [[adaptation (biology)|adaptation]]. This merely confirms that there is no biological distinction between the two strands of the double helix. Typically each strand of a DNA double helix will act as sense and antisense in different regions.

===As viewed by topologists===

Topologists like to note that the juxtaposition of the [[3′ end]] of one DNA strand beside the [[5′ end]] of the other at both ends of a double-helical segment makes the arrangement a &quot;[[crab canon]]".

==Single-stranded DNA (ssDNA) and repair of mutations==

In some [[virus]]es DNA appears in a non-helical, single-stranded form. Because many of the [[DNA repair]] mechanisms of cells work only on paired bases, viruses that carry single-stranded DNA [[genome]]s [[mutation|mutate]] more frequently than they would otherwise. As a result, such species may adapt more rapidly to avoid extinction. The result would not be so favorable in more complicated and more slowly replicating organisms, however, which may explain why only viruses carry single-stranded DNA. These viruses presumably also benefit from the lower cost of replicating one strand versus two.

==History of DNA research==

[[Image:JamesWatson.jpg|thumb|200px|[[James D. Watson|James Watson]] in the [[Cavendish Laboratory]] at the [[University of Cambridge]]]]

The discovery that DNA was the carrier of genetic information was a process that required many earlier discoveries. The existence of DNA was discovered in the mid 19th century. However, it was only in the early 20th century that researchers began suggesting that it might store genetic information. This gained almost universal acceptance after the structure of DNA was elucidated by [[James D. Watson]] and [[Francis Crick]] in their 1953 [[Nature (journal)|''Nature'']] publication. Watson and Crick proposed the [[central dogma]] of molecular biology in 1957, describing the process whereby proteins are produced from [[cell nucleus|nucleic]] DNA. In 1962 Watson, Crick, and [[Maurice Wilkins]] jointly received the [[Nobel Prize]] for their determination of the structure of DNA.

===First isolation of DNA===

Working in the 19th century, biochemists initially isolated DNA and RNA (mixed together) from cell nuclei. They were relatively quick to appreciate the polymeric nature of their "nucleic acid" isolates, but realized only later that nucleotides were of two types--one containing [[ribose]] and the other [[deoxyribose]]. It was this subsequent discovery that led to the identification and naming of DNA as a substance distinct from RNA.

[[Friedrich Miescher]] (1844-1895) discovered a substance he called "nuclein" in 1869. Somewhat later, he isolated a pure sample of the material now known as DNA from the sperm of salmon, and in 1889 his pupil, [[Richard Altmann]], named it "nucleic acid". This substance was found to exist only in the chromosomes.

In 1929 [[Phoebus Levene]] at the [[Rockefeller Institute]] identified the components (the four bases, the sugar and the phosphate chain) and he showed that the components of DNA were linked in the order phosphate-sugar-base. He called each of these units a [[nucleotide]] and suggested the DNA molecule consisted of a string of nucleotide units linked together through the phosphate groups, which are the 'backbone' of the molecule. However Levene thought the chain was short and that the bases repeated in the same fixed order. [[Torbjorn Oskar Caspersson|Torbjorn Caspersson]] and [[Einar Hammersten]] showed that DNA was a polymer.

===Chromosomes and inherited traits===

[[Max Delbrück]], [[Nikolai V. Timofeeff-Ressovsky]], and [[Karl G. Zimmer]] published results in 1935 suggesting that chromosomes are very large molecules the structure of which can be changed by treatment with [[X-ray]]s, and that by so changing their structure it was possible to change the heritable characteristics governed by those chromosomes. In 1937 [[William Astbury]] produced the first [[X-ray diffraction]] patterns from DNA. He was not able to propose the correct structure but the patterns showed that DNA had a regular structure and therefore it might be possible to deduce what this structure was.

In 1943, [[Oswald Theodore Avery]] and a team of scientists discovered that traits proper to the "smooth" form of the ''Pneumococcus'' could be transferred to the "rough" form of the same bacteria merely by making the killed "smooth" (S) form available to the live "rough" (R) form. Quite unexpectedly, the living R ''Pneumococcus'' bacteria were transformed into a new strain of the S form, and the transferred S characteristics turned out to be heritable. Avery called the medium of transfer of traits the [[transforming principle]]; he identified DNA as the transforming principle, and not [[protein]] as previously thought. He essentially redid [[Fredrick Griffith]]'s experiment. In 1953, [[Alfred Hershey]] and [[Martha Chase]] did an experiment ([[Hershey-Chase experiment]]) that showed, in [[T2 phage]], that DNA is the [[genetic material]] (Hershey shared the Nobel prize with Luria).

[[Image:FirstSketchOfDNADoubleHelix.jpg|thumb|200px|[[Francis Crick]]'s first sketch of the [[deoxyribonucleic acid]] double-helix pattern]]

In 1944, the renowned physicist, [[Erwin Schrödinger]], published a brief book entitled ''[[What is Life? (Schrödinger)| What is Life?]]'', where he maintained that chromosomes contained what he called the "hereditary code-script" of life. He added: "But the term code-script is, of course, too narrow. The chromosome structures are at the same time instrumental in bringing about the development they foreshadow. They are law-code and executive power -- or, to use another simile, they are architect's plan and builder's craft -- in one." He conceived of these dual functional elements as being woven into the molecular structure of chromosomes. By understanding the exact molecular structure of the chromosomes one could hope to understand both the "architect's plan" and also how that plan was carried out through the "builder's craft." Three groups took up Schrödinger's challenge to work out the structure of the chromosomes and the question of how the segments of the chromosomes that were conceived to relate to specific traits could

possibly do their jobs.

Just how the presence of specific features in the molecular structure of chromosomes could produce traits and behaviors in living organisms was unimaginable at the time. Because chemical dissection of DNA samples always yielded the same four nucleotides, the chemical composition of DNA appeared simple, perhaps even uniform. Organisms, on the other hand, are fantastically complex individually and widely diverse collectively. Geneticists did not speak of genes as conveyors of "information" in such words, but if they had, they would not have hesitated to quantify the amount of information that genes need to convey as vast. The idea that information might reside in a chemical in the same way that it exists in text--as a finite alphabet of letters arranged in a sequence of unlimited length--had not yet been conceived. It would emerge upon the discovery of DNA's structure, but few researchers imagined that DNA's structure had much to say about genetics.

===Discovery of the structure of DNA===

In the 1950s, three groups made it their goal to determine the structure of DNA. The first group to start was at [[King's College London]] and was led by [[Maurice Wilkins]] and was later joined by [[Rosalind Franklin]]. Another group consisting of [[Francis Crick]] and [[James D. Watson]] was at [[University of Cambridge|Cambridge]]. A third group was at [[Caltech]] and was led by [[Linus Pauling]]. Crick and Watson built physical models using metal rods and balls, in which they incorporated the known chemical structures of the nucleotides, as well as the known position of the linkages joining one nucleotide to the next along the polymer. At King's College Maurice Wilkins and Rosalind Franklin examined [[crystallography|X-ray diffraction]] patterns of DNA fibers. Of the three groups, only the London group was able to produce good quality diffraction patterns and thus produce sufficient quantitative data about the structure.

[[Image:DNA-labels.png|thumb|200px|The chemical structure of DNA]]

====Helix structure====

In 1948 Pauling discovered that many proteins included helical (see [[alpha helix]]) shapes. Pauling had deduced this structure from X-ray patterns and from attempts to physically model the structures. (Pauling was also later to suggest an incorrect three chain helical structure based on Astbury's data.) Even in the initial diffraction data from DNA by Maurice Wilkins, it was evident that the structure involved helices. But this insight was only a beginning. There remained the questions of how many strands came together, whether this number was the same for every helix, whether the bases pointed toward the helical axis or away, and ultimately what were the explicit angles and coordinates of all the bonds and atoms. Such questions motivated the modeling efforts of Watson and Crick.

====Complementary nucleotides====

In their modeling, Watson and Crick restricted themselves to what they saw as chemically and biologically reasonable. Still, the breadth of possibilities was very wide. A breakthrough occurred in 1952, when [[Erwin Chargaff]] visited Cambridge and inspired Crick with a description of experiments Chargaff had published in 1947. Chargaff had observed that the proportions of the four nucleotides vary between one DNA sample and the next, but that for particular pairs of nucleotides &mdash; adenine and thymine, guanine and cytosine &mdash; the two nucleotides are always present in equal proportions.

====Watson and Crick's model====

[[Image:DNA Model Crick-Watson.jpg|thumb|200px|right|Crick and Watson DNA model built in 1953, currently on display at the [[Science Museum (London)|National Science Museum]] in London.]]

[[James D. Watson|Watson]] and [[Francis Crick|Crick]] had begun to contemplate double helical arrangements, but they lacked information about the amount of twist (pitch) and the distance between the two strands. [[Rosalind Franklin]] had to disclose some of her findings for the [[Medical Research Council]] and Crick saw this material through [[Max Perutz|Max Perutz's]] links to the MRC. Franklin's work confirmed that the phosphate "backbone" was on the outside of the molecule and also gave an insight into its symmetry, in particular that the two helical strands ran in opposite directions.

Watson and Crick were again greatly assisted by more of Franklin's data. This is controversial because Franklin's critical X-ray pattern was shown to Watson and Crick without Franklin's knowledge or permission. Wilkins showed the famous Photo 51 of the much simpler ''B'' type of DNA to Watson at his lab immediately after Watson had been unsuccessful in asking Franklin to collaborate to beat Pauling in finding the structure.

From the data in photograph 51 Watson and Crick were able to discern that not only was the distance between the two strands constant, but also to measure its exact value of 2 nanometres. The same photograph also gave them the 3.4 nanometre-per-10 bp "pitch" of the helix.

The final insight came when Crick and Watson saw that a complementary pairing of the bases could provide an explanation for Chargaff's puzzling finding. However the structure of the bases had been incorrectly guessed in the textbooks as the [[enol]] [[tautomer]] when they were more likely to be in the [[keto]] form. When [[Jerry Donohue]] pointed this fallacy out to Watson, Watson quickly realised that the pairs of adenine and thymine, and guanine and cytosine were almost identical in shape and so would provide equally sized 'rungs' between the two strands. Watson and Crick worked to develop a physical model of the double-helical structure out of wire which they used to confirm that the distances between the molecules were permissable. With the base-pairing, the Watson and Crick quickly converged upon a model, which they announced before Franklin herself had published any of her work.

Franklin was herself two steps away from the solution. She had not guessed the base-pairing and had not appreciated the implications of the symmetry that she had described. However she had been working almost alone and did not have regular contact with a partner like Crick and Watson, and with other experts such as Jerry Donohue. Her notebooks show that she was aware both of Jerry Donohue's work concerning tautomeric forms of bases (she had used the keto forms for three of the bases) and of Chargaff's work.

The disclosure of Franklin's data to Watson has angered some people who believe Franklin did not receive due credit at the time and that she might have discovered the structure on her own before Crick and Watson. In Crick and Watson's famous paper in Nature in 1953, they said that their work had been stimulated by the work of Wilkins and Franklin, whereas it had been the basis of their work. However they had agreed with Wilkins and Franklin that they all should publish papers in the same issue of ''Nature'' in support of the proposed structure. Additionally, in his autobiography, ''[[The Double Helix]]'', Watson describes Franklin in very unflattering terms (commenting derisively on her lack of "feminine" traits) and all but implies that her work actually impaired that of Wilkins.

===="Central Dogma"====

Watson and Crick's model attracted great interest immediately upon its presentation. Arriving at their conclusion on [[February 21]] [[1953]], Watson and Crick made their first announcement on [[February 28]]. Their paper ''A Structure for Deoxyribose Nucleic Acid''<ref>Watson and Crick, 1953</ref> was published on April 25. In an influential presentation in 1957, Crick laid out the "[[Central Dogma]]", which foretold the relationship between DNA, RNA, and proteins, and articulated the "sequence hypothesis." A critical confirmation of the replication mechanism that was implied by the double-helical structure followed in 1958 in the form of the [[Meselson-Stahl experiment]]. Work by Crick and coworkers showed that the genetic code was based on non-overlapping triplets of bases, called codons, and [[Har Gobind Khorana]] and others deciphered the [[genetic code]] not long afterward. These findings represent the birth of [[molecular biology]].

[[James D. Watson|Watson]], [[Francis Crick|Crick]], and [[Maurice Wilkins|Wilkins]] were awarded the 1962 [[Nobel Prize for Physiology or Medicine]] for discovering the molecular structure of DNA, by which time [[Rosalind Franklin|Franklin]] had died from cancer at 37. Nobel prizes are not awarded posthumously; had she lived, the difficult decision over whom to jointly award the prize would have been complicated as the prize can only be shared between a maximum of three; but because their work could be considered to be chemistry, it is conceivable that [[Maurice Wilkins|Wilkins]] and [[Rosalind Franklin|Franklin]] could have been awarded the [[Nobel Prize for Chemistry]] instead; see Graeme Hunter's biography of Sir Lawrence Bragg for more information on how scientists were nominated for Nobel Prizes.

==References==

===Citations===

<div class="references-small">

<references/>

</div>

===General references===

* [[Robert Olby]]; "The Path to The Double Helix: Discovery of DNA"; first published in 0ctober 1974 by MacMillan, with foreword by Francis Crick; ISBN: 046681173; the definitive DNA textbook, revised in 1994, with a 9 page postscript.

* [[Matt Ridley|Ridley, Matt]]; ''Francis Crick: Discoverer of the Genetic Code (Eminent Lives)'' first published in June 2006 in the USA and then to be in the U.K. September 2006, by HarperCollins Publishers; 192 pp, ISBN 006082333X

* Watson, James D. and Francis H.C. Crick. [http://www.nature.com/nature/dna50/watsoncrick.pdf A structure for Deoxyribose Nucleic Acid] (PDF). ''[[Nature (journal)|Nature]]'' 171, 737&ndash;738, [[25 April]] [[1953]].

* Watson, James D. ''DNA: The Secret of Life'' ISBN 0375415467.

* Watson, James D. [[The Double Helix|The Double Helix: A Personal Account of the Discovery of the Structure of DNA (Norton Critical Editions)]]. ISBN 0393950751

* Chomet, S. (Ed.), DNA Genesis of a Discovery, ''Newman-Hemisphere Press, London, 1994.

* Delmonte, C.S. and Mann, L.R.B. [http://www.ias.ac.in/currsci/dec102003/1564.pdf Variety in DNA tertiary structure]. Current Science, 85 (11), 1564&ndash;1570, 10 December 2003.

*Miller, Kenneth R., and Levin, Joseph. ''Biology''. Saddle River, New Jersey: Prentice Hall, 2002.

==External links==

*[http://www.billboard.com/bbcom/news/article_display.jsp?vnu_content_id=1003557485 'R. Kelly Previews New Album On The Phone']

*[http://www.dnahack.com/index.html DNA hack: The website for Amateur Genetic Engineering]

*[http://www.packer34.freeserve.co.uk/rememberingfranciscrickacelebration.htm on Francis Crick]

*[http://www.packer34.freeserve.co.uk/selectedTATAwebsites.htm First press stories on DNA]

*[http://en.wikipedia.org/wiki/Image:Rosalindfranklinsjokecard.jpg 'Death' of DNA Helix (Crystaline) joke funeral card].

*[http://www.nature.com/nature/dna50/archive.html Double helix: 50 years of DNA], [[Nature (journal)|Nature]].

*[http://www.genome.gov/10506367 U.S. National DNA Day] Watch videos and participate in real-time chat with top scientists

*[http://www.genome.gov/10506718 Genetic Education Modules for Teachers] ''DNA from the Beginning'' Study Guide

*[http://www.genome.gov/glossary.cfm Talking Glossary of Genetic Terms] In Spanish, too

*[http://osulibrary.oregonstate.edu/specialcollections/coll/pauling/dna/index.html Linus Pauling and the Race for DNA]

*[http://www.bbc.co.uk/bbcfour/audiointerviews/profilepages/crickwatson1.shtml Listen to Francis Crick and James Watson talking on the BBC in 1962, 1972, and 1974]

*[http://news.bbc.co.uk/1/hi/sci/tech/2949629.stm 17 April, 2003, BBC News: Most ancient DNA ever?]

*[http://www.whatsnextnetwork.com/health/index.php?cat=61 Latest Advances In Gene Research]

*[http://www.dna-research.org DNA Research News]

*[http://www.dnakin.com Using DNA in Genealogical Research]

*[http://www.dnai.org DNA Interactive] (requires [[Macromedia Flash]])

*[http://nist.rcsb.org/pdb/molecules/pdb23_1.html DNA: PDB molecule of the month]

*[http://www.fidelitysystems.com/Unlinked_DNA.html DNA under electron microscope]

*[http://www.ccrnp.ncifcrf.gov/~toms/LeftHanded.DNA.html Left-handed DNA Hall of Fame]

*[http://www.myfirstbookaboutdna.com My First Book About DNA] Designed for children to learn more about DNA.

*{{dmoz|Science/Biology/Biochemistry_and_Molecular_Biology/Biomolecules/Nucleic_Acids/|Nucleic Acids}}

*[http://www.zytologie-online.net/dna.php DNA Replication and Translation / Cell Biology]

*[http://dnawiz.com/ DNA Articles] DNA Articles and Information collected from various sources.

{{Nucleic acids}}

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